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https://github.com/MillironX/nf-core_modules.git
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daab0a77dd
* Update main.nf * Update meta.yml * Re-add logos as not staged in a way that works with MultiQC config files * Update main.nf * Remove now unnecessary input channel * Remove unused channel from tests * Update hAMRonization to 1.1.1 and add hAMRonization farGene * Fix hamronizatio ntests * Prettier * Fix fargene linting * Correct file * Fix fargene output * Apply suggestions from code review Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com> * Fix summarise tests * Prettier Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
9 lines
1.1 KiB
YAML
9 lines
1.1 KiB
YAML
- name: hamronization amrfinderplus test_hamronization_amrfinderplus
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command: nextflow run ./tests/modules/hamronization/amrfinderplus -entry test_hamronization_amrfinderplus -c ./tests/config/nextflow.config -c ./tests/modules/hamronization/amrfinderplus/nextflow.config
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tags:
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- hamronization
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- hamronization/amrfinderplus
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files:
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- path: output/hamronization/test.tsv
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contains:
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- "input_file_name gene_symbol gene_name reference_database_name reference_database_version reference_accession analysis_software_name analysis_software_version genetic_variation_type antimicrobial_agent coverage_percentage coverage_depth coverage_ratio drug_class input_gene_length input_gene_start input_gene_stop input_protein_length input_protein_start input_protein_stop input_sequence_id nucleotide_mutation nucleotide_mutation_interpretation predicted_phenotype predicted_phenotype_confidence_level amino_acid_mutation amino_acid_mutation_interpretation reference_gene_length reference_gene_start reference_gene_stop reference_protein_length reference_protein_start reference_protein_stop resistance_mechanism strand_orientation sequence_identity"
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